TangleSolve



  1. Download Java plug-in to run the applet version.
  2. Download Java Run-time to run the application version.

If the Java plug-in and the Java run-time environment are not installed in your system, then your system administrator has to do it (unless you manage your own computer) using the same links as before.

  1. Applet Version 1 (with knot/link illustrations: SLOW): follow the link.
  2. Application Version (this version will allow you to run the program locally from your hard drive): save the file to your local drive by right-clicking on the link, selecting "save link as" and chosing the target directory. From your local directory containing the file GInterface.jar, type java-jar GInterface.jar into the comand line. Use the same command when working in UNIX. Unfortunately this version is not working properly in Linux




Reference: Y. Saka, M. Vazquez, TangleSolve: topological analysis of site-specific recombination, Bioinformatics (2002) 18:1011-1012 (PDF)



Site-specific recombination plays a central role in many biological processes. The enzymes responsible for it, called site-specific recombinases, fill a role of molecular scissors in that they are able to cleave double-stranded DNA. In a single enzymatic event the enzyme(s) recognize specific recombination sites, mediate a double-stranded break at the core regions of each of the sites, recombine the lose ends, and reseal the recombined strands as illustrated in the following figure:

In vitro experiments of site-specific recombination on circular DNA substrates with a fixed topology often yield spectra of knotted or catenated molecules. In order to help understand the enzymatic mechanism, the topology of the DNA products of recombination is analyzed using the tangle model [T1-T4]. The tangle model converts the biological problem of solving the enzymatic action, into the mathematical problem of computing the geometrical and topological configuration of the DNA molecule before, during and after the recombinaiton event.

TangleSolve is a Java applet/application which implements the tangle model and offers an easy-to-use graphical interface for analyzing and visualizing recombination mechanisms. The following example illustrates a tangle equation and it's graphical representation within TangleSolve:


N(Of+Ob+P) = 632*


Of = (0); Ob = (2,2,2); P = (0); 632* = < 1,1,2,1,1 >



Standard knot diagram for 632* from D.Rolfsen's Knots and links, [K1]

ScreenShot of the application

  • Simple Tutorial
    •  References:

    Click here to read a few words about the people involved in this project, and to see the acknowledgements.

    Questions? mariel@math.berkeley.edu